Skip to main content

Table 6 AA-15-DNA

From: Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

AA-15-DNA UCD NCD CD
  UPGMA NJ UPGMA NJ UPGMA NJ
Gzip 4 5 6 9 6 9
Bzip2 6 5 6 5 6 5
PPMd16 4 3 4 3 4 5
PPMd8 4 5 4 5 4 5
PPMd4 8 9 10 13 8 13
PPMd2 24 23 24 23 24 23
Gencompress 4 3 4 3 4 5
Huffman 22 21 22 21 22 23
Ac fast 24 21 22 21 24 23
Rc fast 24 23 22 21 24 21
Ac med. 18 23 24 21 22 21
Rc med. 24 23 22 19 24 21
Ac slow 24 15 16 15 16 17
Rc slow 18 17 14 17 12 17
BwtRleHuff 4 5 4 5 4 5
BwtMtfRleHuff 4 5 4 5 4 5
BwtRleAc fast 6 5 6 5 6 5
BwtMtfRleAc fast 4 5 4 5 4 5
BwtRleRc fast 6 5 6 5 6 5
BwtMtfRleRc fast 4 5 4 5 4 5
BwtRleRc med. 6 5 6 5 6 5
BwtMtfRleRc med. 4 5 4 5 4 5
BwtRleRc slow 6 5 6 5 6 5
BwtMtfRleRc slow 4 5 4 5 4 5
BwtWavelet 6 5 6 5 6 5
  1. Experimental results for the AA-15-DNA data set, with the UCD (left), NCD (middle), and CD (right) distance. For each compression algorithm, we report the partition distance for both UPGMA and NJ methods. Since the data set contains 15 species, the partition distance ranges from 0 to 50 in this case.